Publications

Our Publications

Information about development of CytoSolve™ has evinced keen interest among the research community world-wide. A number of papers have been written on the CytoSolve™ platform and its components. Researchers in the fields of computational biology and development of drug and treatment plans are using CytoSolve™ to build their thesis.

You can view and read papers published on CytoSolve™ and papers published by other researchers that cite CytoSolve™ on this page.

Papers

Multi-Criteria Decision Analysis Model for Assessing the Risk from Multi-Ingredient Dietary Supplements (MIDS)

Military personnel use dietary supplements (DS) for performance enhancement, bodybuilding, weight loss, and to maintain health. Adverse events, including cardiovascular (CV) effects, have been reported in military personnel taking supplements. Previous research determined that ingestion of multi-ingredient dietary supplements (MIDS), can lead to signals of safety concerns.

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In-Silico Analysis & In-Vivo Results Concur on Glutathione Depletion in Glyphosate Resistant GMO Soy, Advancing a Systems Biology Framework for Safety Assessment of GMOs

This study advances previous efforts towards development of computational systems biology, in silico, methods for biosafety assessment of genetically modified organisms (GMOs). C1 metabolism is a critical molecular system in plants, fungi, and bacteria. In our previous research, critical molecular systems of C1 metabolism were identified and modeled using CytoSolve?, a platform for in silico analysis.

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Do GMOs Accumulate Formaldehyde and Disrupt Molecular Systems Equilibria? Systems Biology May Provide Answers

Safety assessment of genetically modified organisms (GMOs) is a contentious topic. Proponents of GMOs assert that GMOs are safe since the FDA’s policy of substantial equivalence considers GMOs “equivalent” to their non-GMO counterparts, and argue that genetic modification (GM) is simply an extension of a “natural” process of plant breeding, a form of “genetic modification”, though done over longer time scales.

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Services-Based Systems Architecture for Modeling the Whole Cell: A Distributed Collaborative Engineering Systems Approach

Modeling the whole cell is a goal of modern systems biology. Current approaches are neither scalable nor flexible to model complex cellular functions. They do not support collaborative development, are monolithic and, take a primarily manual approach of combining each biological pathway model’s software source code to build one large monolithic model that executes on a single computer.

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Multiscale Mathematical Modeling to Support Drug Development

It is widely recognized that major improvements are required in the methods currently being used to develop new therapeutic drugs. The time from initial target identification to commercialization can be 10–14 years and incur a cost in the hundreds of millions of dollars. Even after substantial investment, only 30–40% of the candidate compounds entering clinical trials are successful.

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Pericytes of the neurovascular unit: key functions and signaling pathways

Pericytes are vascular mural cells embedded in the basement membrane of blood microvessels. They extend their processes along capillaries, pre-capillary arterioles and post-capillary venules. CNS pericytes are uniquely positioned in the neurovascular unit between endothelial cells, astrocytes and neurons.

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In Silico Modeling of Shear-Stress-Induced Nitric Oxide Production in Endothelial Cells through Systems Biology

Nitric oxide (NO) produced by vascular endothelial cells is a potent vasodilator and an antiinflammatory mediator. Regulating production of endothelial-derived NO is a complex undertaking, involving multiple signaling and genetic pathways that are activated by diverse humoral and biomechanical stimuli.

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OREMPdb: A Semantic Dictionary Of Computational Pathway Models

The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web.

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CytoSolve™: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models

A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models’ source codes to create a large monolithic model (computer program) that runs on a single computer.

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A Distributed Computational Architecture for Integrating Multiple Biomolecular Pathways

Biomolecular pathways are building blocks of cellular biochemical function. Computational biology is in rapid transition from diagrammatic representation of pathways to quantitative and predictive mathematical models, which span time-scales, knowledge domains and spatial-scales. This transition is being accelerated by high-throughput experimentation which isolates reactions and their corresponding rate constants.

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Integrating an Ensemble of Distributed Biochemical Network Models

A new system for integrating an ensemble of distributed biochemical network models is presented.

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Citations

Nature Publishing Group – Combinatorial Drug Therapy for Cancer

Computational protocols, such as CytoSolve, allow the combination of alternative models and generation of consensus hypotheses.

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Setting a Research Agenda for Progressive MS: The International Collaborative on Progressive MS

Indeed, computational biology is shifting from diagrammatic representation of pathways to mathematical models. These techniques hold promise to provide the tools for interpreting genetic data across different knowledge domains.

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Contribution of Genome-Wide Association Studies to Scientific Research: A Pragmatic Approach to Evaluate Their Impact

The factual value of genome-wide association studies (GWAS) for the understanding of multifactorial diseases is a matter of intense debate. Practical consequences for the development of more effective therapies do not seem to be around the corner. Here we propose a pragmatic and objective evaluation of how much new biology is arising from these studies, with particular attention to the information that can help prioritize therapeutic targets.

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The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models

The complexity and multiscale nature of the mammalian immune response provides an excellent test bed for the potential of mathematical modeling and simulation to facilitate mechanistic understanding. Historically, mathematical models of the immune response focused on subsets of the immune system and/or specific aspects of the response. Mathematical models have been developed for the humoral side of the immune response, or for the cellular side, or for cytokine kinetics, but rarely have they been proposed to encompass the overall system complexity. We propose here a framework for integration of subset models, based on a system biology approach.

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